High-yield and high-purity amide bond formation using DMTMM PF6 for DNA-encoded libraries.

In this study, we report on the ability of DMTMM PF6 to improve the amidation reaction. The on-DNA amidation reaction using DMTMM PF6 demonstrates higher conversion rates than those using HATU or DMTMM Cl, particularly with challenging sterically hindered amines and carboxylic acids. The developed method enables the expansion of available building blocks and the efficient synthesis of high-purity DNA-encoded libraries.

Molecular Insights into Female Hybrid Sterility in Interspecific Crosses between Drosophila melanogaster and Drosophila simulans.

Species of the genus Drosophila have served as favorite models in speciation studies; however, genetic factors of interspecific reproductive incompatibility are under-investigated. Here, we performed an analysis of hybrid female sterility by crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis and molecular, cellular, and genetic approaches, we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis, and functional defects of oogenesis in hybrids. Premature germline stem cell loss was the most prominent defect of oogenesis in hybrid ovaries. Because of the differential expression of genes encoding piRNA pathway components, rhino and deadlock, the functional RDCmel complex in hybrid ovaries was not assembled. However, the activity of the RDCsim complex was maintained in hybrids independent of the genomic origin of piRNA clusters. Despite the identification of a cohort of overexpressed TEs in hybrid ovaries, we found no evidence that their activity can be considered the main cause of hybrid sterility. We revealed a complicated pattern of Vasa protein expression in the hybrid germline, including partial AT-chX piRNA targeting of the vasasim allele and a significant zygotic delay in vasamel expression. We arrived at the conclusion that the hybrid sterility phenotype was caused by intricate multi-locus differences between the species.

The impact of libraries and informationists on patient and population care: a mixed-methods study.

Objective: While several studies have examined the effectiveness of librarian interactions with clinicians and impact of librarians on patient care, no studies have explored a library's effects on population care. The goal of this study was to investigate the library's impact on both patient and population care. Methods: Using a sequential exploratory mixed-methods design, we first interviewed a small set of clinicians and researchers active in patient and population care. Based on the themes that we discovered through coding the interviews, we created a survey that was sent to faculty in the health sciences and the health system. Results: We collected data from a representative sample of our population. We discovered that all respondents value the library and informationists, using our services most for teaching, publishing, presenting, and professional development. Conclusion: We now have data to support our value to our population and to show where we can do more work to improve the use of our services. Our study shows the value of doing a mixed-methods sequential exploration in which themes that are important to our user community were identified prior to launching a large-scale survey.

Developing and conducting a language inclusivity assessment on a health science library's website, LibGuides, and signage.

Background: A Diversity, Equity, and Inclusion (DEI) Team at a university health science library created a checklist for inclusive language and conducted an assessment of their library's website, LibGuides, and physical and digital signage. Inclusive language was defined as "language that is free from words, phrases or tones that reflect prejudiced, stereotyped or discriminatory views of particular people or groups". Case Presentation: The 32-item checklist facilitated the identification of gendered language, stereotypes, ableist language, racist language, stigmatizing language, slang, acronyms, and out-of-date terminology regarding physical and mental health conditions. From the library's website, 20 instances were noted for which improvements were necessary. Out of the 130 LibGuides reviewed, 23 LibGuides had no changes needed and 107 had changes identified relating to language inclusivity (14 strongly recommended changes and 116 suggested changes). Regarding the signage, one flyer was removed for reprinting. Conclusion: The checklist enabled the team to implement a number of improvements to the library's website and LibGuides. The checklist has been shared with Library Technology Services and the wider campus libraries' Usability Committee for future use, and has also been added to the DEI Team's LibGuide for use by others outside of the university.

PxBLAT: an efficient python binding library for BLAT.

BACKGROUND: With the surge in genomic data driven by advancements in sequencing technologies, the demand for efficient bioinformatics tools for sequence analysis has become paramount. BLAST-like alignment tool (BLAT), a sequence alignment tool, faces limitations in performance efficiency and integration with modern programming environments, particularly Python. This study introduces PxBLAT, a Python-based framework designed to enhance the capabilities of BLAT, focusing on usability, computational efficiency, and seamless integration within the Python ecosystem. RESULTS: PxBLAT demonstrates significant improvements over BLAT in execution speed and data handling, as evidenced by comprehensive benchmarks conducted across various sample groups ranging from 50 to 600 samples. These experiments highlight a notable speedup, reducing execution time compared to BLAT. The framework also introduces user-friendly features such as improved server management, data conversion utilities, and shell completion, enhancing the overall user experience. Additionally, the provision of extensive documentation and comprehensive testing supports community engagement and facilitates the adoption of PxBLAT. CONCLUSIONS: PxBLAT stands out as a robust alternative to BLAT, offering performance and user interaction enhancements. Its development underscores the potential for modern programming languages to improve bioinformatics tools, aligning with the needs of contemporary genomic research. By providing a more efficient, user-friendly tool, PxBLAT has the potential to impact genomic data analysis workflows, supporting faster and more accurate sequence analysis in a Python environment.

In vivo selection in non-human primates identifies AAV capsids for on-target CSF delivery to spinal cord.

Systemic administration of adeno-associated virus (AAV) vectors for spinal cord gene therapy has challenges including toxicity at high doses and pre-existing immunity that reduces efficacy. Intrathecal (IT) delivery of AAV vectors into cerebral spinal fluid can avoid many issues, although distribution of the vector throughout the spinal cord is limited, and vector entry to the periphery sometimes initiates hepatotoxicity. Here we performed biopanning in non-human primates (NHPs) with an IT injected AAV9 peptide display library. We identified top candidates by sequencing inserts of AAV DNA isolated from whole tissue, nuclei, or nuclei from transgene-expressing cells. These barcoded candidates were pooled with AAV9 and compared for biodistribution and transgene expression in spinal cord and liver of IT injected NHPs. Most candidates displayed increased retention in spinal cord compared with AAV9. Greater spread from the lumbar to the thoracic and cervical regions was observed for several capsids. Furthermore, several capsids displayed decreased biodistribution to the liver compared with AAV9, providing a high on-target/low off-target biodistribution. Finally, we tested top candidates in human spinal cord organoids and found them to outperform AAV9 in efficiency of transgene expression in neurons and astrocytes. These capsids have potential to serve as leading-edge delivery vehicles for spinal cord-directed gene therapies.

Healthy Me, Healthy Planet: Evaluation of a pilot planetary health library program.

ISSUE ADDRESSED: The Healthy Me, Healthy Planet program was an evidence-informed pilot program conducted by a local libraries to promote the health co-benefits of action on climate change. BACKGROUND: An impact evaluation of the Healthy Me, Healthy Planet program was conducted using a mixed methods research design including pre-, during, and post-program surveys and online focus groups. METHODS: The evaluation included 136 participants aged 18+ years who were able to understand and communicate in English or simplified Chinese language. Descriptive analyses of the survey data were integrated with thematic analyses of focus group (N = 2) data to generate key themes. RESULTS: Key impacts included individual and organisational capacity building, personal and social well-being, and pro-environmental knowledge, attitudes, and behaviour. Impacts on program participants included increased confidence, motivation, positive feelings, and personal well-being after taking part in the Healthy Me, Healthy Planet program. Participants reported enhanced social connections, mental well-being, and environmental benefits such as engaging within the community on environmental issues and feeling inspired to make sustainable lifestyle changes. CONCLUSION: Libraries play a key role in promoting the health of people and planet in the community because they are a trusted, safe, and supportive community setting, a curator of credible and reliable evidence-based information on health and planetary topics and a local and free provider for skills and literacy development. SO WHAT: The evaluation of the pilot suggests that participants improved their capacity to practice sustainable living and it is recommended that this program be expanded to other library settings to enhance community connection and support local planetary health initiatives.

Exploring uncharted territory: new frontiers in environmental DNA for tropical fisheries management.

Tropical ecosystems host a significant share of global fish diversity contributing substantially to the global fisheries sector. Yet their sustainable management is challenging due to their complexity, diverse life history traits of tropical fishes, and varied fishing techniques involved. Traditional monitoring techniques are often costly, labour-intensive, and/or difficult to apply in inaccessible sites. These limitations call for the adoption of innovative, sensitive, and cost-effective monitoring solutions, especially in a scenario of climate change. Environmental DNA (eDNA) emerges as a potential game changer for biodiversity monitoring and conservation, especially in aquatic ecosystems. However, its utility in tropical settings remains underexplored, primarily due to a series of challenges, including the need for a comprehensive barcode reference library, an understanding of eDNA behaviour in tropical aquatic environments, standardized procedures, and supportive biomonitoring policies. Despite these challenges, the potential of eDNA for sensitive species detection across varied habitats is evident, and its global use is accelerating in biodiversity conservation efforts. This review takes an in-depth look at the current state and prospects of eDNA-based monitoring in tropical fisheries management research. Additionally, a SWOT analysis is used to underscore the opportunities and threats, with the aim of bridging the knowledge gaps and guiding the more extensive and effective use of eDNA-based monitoring in tropical fisheries management. Although the discussion applies worldwide, some specific experiences and insights from Indian tropical fisheries are shared to illustrate the practical application and challenges of employing eDNA in a tropical context.

Community health information needs assessment in the mid-south region of the United States indicates new roles for public libraries.

BACKGROUND: Libraries provide public access to information that may be used to inform healthcare decisions. Exploring the health information needs of library-users could improve community health outcomes, especially during times of crisis like the COVID-19 pandemic. OBJECTIVE: The purpose of this study was to identify the health information needs of library-users to explore the potential role of libraries in advancing community health. METHODS: A quantitative, descriptive, cross-sectional survey was employed. RESULTS: One hundred and fifty participants in the (Memphis) Tennessee metropolitan area, ranging from 18 to 84 years of age, completed the survey between September 2020 and April 2021. Most respondents reported seeking physical and mental health-related information from libraries. In addition, nearly half of respondents reported delaying medical care due to risk of exposure to COVID-19, cost or appointment issues. DISCUSSION: Study results indicated that there were urgent health information needs among library-users in this community, that COVID-19 further limited or delayed access to information, and that library-users accessed health information during library visits. CONCLUSION: Public libraries have the potential to serve as information hubs to improve community health outcomes. Additional research should be conducted to collect qualitative community health information needs and the ways in which public library systems can address them.

Elucidating the Unconventional Binding Mode of a DNA-Encoded Library Hit Provides a Blueprint for Sirtuin 6 Inhibitor Development.

Sirtuin 6 (Sirt6), an NAD+-dependent deacylase, has emerged as a promising target for aging-related diseases and cancer. Advancing the medicinal chemistry of Sirt6 modulators is crucial for the development of chemical probes aimed at unraveling the intricate biological functions of Sirt6 and unlocking its therapeutic potential. A proprietary DNA-encoded library yielded Sirt6 inhibitor 2-Pr, displaying remarkable inhibitory activity and isoform-selectivity, and featuring a chemical structure distinct from reported Sirt6 modulators. In this study, we explore the inhibitory mechanism of 2-Pr, evaluating the impact of chemical modifications and presenting a crystal structure of the Sirt6/ADP-ribose/2-Pr complex. Notably, co-crystal structure analysis reveals an unexpected and unprecedented binding mode of Sirt6, with 2-Pr spanning the acyl channel of the enzyme, extending into the acetyl-lysine binding pocket, and reaching toward the C-site. This unique binding mode guides potential avenues for developing potent and selective Sirt6 inhibitors.

Public libraries to promote public health and wellbeing: a cross-sectional study of community-dwelling adults.

BACKGROUND: Libraries in the UK have evolved from traditional book-lending institutions into dynamic community hubs, This study aims to explore the potential of libraries to act as community hubs to promote mental and physical health and wellbeing of community-dwelling adults, drawing on insights from both library users and library staff in England. DESIGN: A mixed-method, cross-sectional study using online survey and interviews with community-dwelling adults and library staff. METHODS: We collected data using a 14-item electronic survey and interviews with library users and staff to gauge perceptions. Descriptive statistics and thematic analysis were used to identify key trends and emergent themes. RESULTS: We included 605 respondents from the survey and interviewed 12 library users and staff. Libraries remain popular and are considered a 'safe place by members of the community, regardless of their frequency of service usage irrespective of whether they are frequent users of services. However, a lack of awareness among library users about community-facing services could act as a hurdle to improving community health and wellbeing. Targeted engagement with residents is needed to increase awareness of libraries' services, including community interventions to help tackle loneliness and inequalities in digital and health literacy. Library staff often did not feel involved in important decision-making. Various barriers, drivers and practical recommendations were identified to leverage libraries as hubs to promote community health and wellbeing. CONCLUSION: Libraries already offer a variety of resources that directly or indirectly support the health and wellbeing of community-dwelling adults and young people. However, public awareness of these services is limited. As we navigate post-pandemic recovery, libraries can serve as platforms for community engagement, fostering resilience, mental health support and reducing social isolation. Recognising libraries' untapped potential can lead to healthier communities and improved wellbeing.

Improving LibGuides at a Health Sciences Library: A Case Study.

While LibGuides are widely used in libraries to curate resources for users, there are a number of common problems, including maintenance, design and layout, and curating relevant and concise content. One health sciences library sought to improve our LibGuides, consulting usage statistics, user feedback, and recommendations from the literature to inform decision making. Our team recommended a number of changes to make LibGuides more usable, including creating robust maintenance and content guidelines, scheduling regular updates, and various changes to the format of the guides themselves to make them more user-friendly.

Systems Librarianship Through the Lens of an Open Systems Framework in a Hospital Library Setting: A Case Report.

Systems librarianship, when merged with the position of informationist, evolves into the identity of the systems informationist in the hospital setting. The Health Sciences Library at Geisinger has successfully implemented a systems informationist role within an open systems framework. The duties of the systems informationist are framed here using: input for information-seeking behavior; throughput of clinical support for patient care; output by user experience in research and education; and feedback to elevate operational excellence. This case report contributes a focused approach to systems librarianship, providing examples for other hospital libraries that may be interested in developing their own Systems Services.

How Ohio public library systems respond to opioid-related substance use: a descriptive analysis of survey results.

BACKGROUND: Public libraries in the United States have experienced increases in opioid-related substance use in their communities and on their premises. This includes fatal and non-fatal overdose events. Some libraries have adopted response measures in their branches to deter substance use or prevent overdose. A small number of libraries around the nation have decided to stock the opioid antagonist naloxone (Narcan) for staff to administer to patrons who experience overdose. This response measure has generated extensive media attention. Although Ohio ranks fourth in age-adjusted drug mortality rate in the United States, there has been no investigation of whether Ohio libraries are observing opioid-related transactions, consumption, and/or overdose events, or which measures they have adopted in response to these activities. We conducted a multimethod survey with Ohio public library directors to identify the response measures they have adopted. We present descriptive findings from the quantitative and qualitative items in our survey. METHODS: We conducted a cross-sectional 54-item multimethod survey of public library system directors (one per system) in Ohio. Directors of each of Ohio's public library systems were invited to participate via email. RESULTS: Of 251 library systems, 56 responded (22.3% response rate), with 34 respondents (60.7%) indicating awareness of opioid-related transactions, consumption, and/or overdose on their premises. Most (n = 43, 76.8%) did not stock naloxone in their buildings. Over half (n = 34, 60.7%) reported implementing one or more non-naloxone response measures. These measures focus on improving security for staff and patrons, deterring opioid-related transactions (purchases and exchanges) and consumption, and providing educational events on substance use. Nearly half (n = 25, 47.2%) partner with community organizations to provide opioid response measures. A similar proportion reported adequate funding to respond to opioid-related substance use (n = 23, 45.1%), and most (n = 38, 74.5%) reported adequate support from their boards and communities. Few respondents have implemented evaluations of their response measures. CONCLUSIONS: Ohio public libraries are responding to evidence of opioid-related transactions, consumption, and/or overdose on their premises with a range of measures that focus on substance use prevention and deterrence. Most Ohio library systems do not stock naloxone. Respondents indicated they prefer to call 911 and let first responders handle overdose events. The majority of respondents indicated their library systems have political capacity to respond to evidence of opioid-related substance use on their premises, but have limited operational and functional capacity. Findings suggest the need to revisit assumptions that public libraries are willing to stock naloxone to respond to overdose events, and that libraries have the resources to respond robustly to opioid-related transactions, consumption, and/or overdose on their premises.

Library Screening, In Vivo Confirmation, and Structural and Bioinformatic Analysis of Pentapeptide Sequences as Substrates for Protein Farnesyltransferase.

Protein farnesylation is a post-translational modification where a 15-carbon farnesyl isoprenoid is appended to the C-terminal end of a protein by farnesyltransferase (FTase). This process often causes proteins to associate with the membrane and participate in signal transduction pathways. The most common substrates of FTase are proteins that have C-terminal tetrapeptide CaaX box sequences where the cysteine is the site of modification. However, recent work has shown that five amino acid sequences can also be recognized, including the pentapeptides CMIIM and CSLMQ. In this work, peptide libraries were initially used to systematically vary the residues in those two parental sequences using an assay based on Matrix Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). In addition, 192 pentapeptide sequences from the human proteome were screened using that assay to discover additional extended CaaaX-box motifs. Selected hits from that screening effort were rescreened using an in vivo yeast reporter protein assay. The X-ray crystal structure of CMIIM bound to FTase was also solved, showing that the C-terminal tripeptide of that sequence interacted with the enzyme in a similar manner as the C-terminal tripeptide of CVVM, suggesting that the tripeptide comprises a common structural element for substrate recognition in both tetrapeptide and pentapeptide sequences. Molecular dynamics simulation of CMIIM bound to FTase further shed light on the molecular interactions involved, showing that a putative catalytically competent Zn(II)-thiolate species was able to form. Bioinformatic predictions of tetrapeptide (CaaX-box) reactivity correlated well with the reactivity of pentapeptides obtained from in vivo analysis, reinforcing the importance of the C-terminal tripeptide motif. This analysis provides a structural framework for understanding the reactivity of extended CaaaX-box motifs and a method that may be useful for predicting the reactivity of additional FTase substrates bearing CaaaX-box sequences.

Peptide libraries: from epitope mapping to in-depth high-throughput analysis.

Peptide arrays are a valuable instrument in the characterization of protein-protein interactions (PPIs) and immunogenic regions. New methods were developed to exploit the high-throughput potential of peptide arrays to obtain more in-depth information, replacing traditional resource-intensive experiments. Here, we discuss the recent advances in peptide-array-based technologies and the remaining challenges.

Advancement in the development of single chain antibodies using phage display technology.

Phage display technology has become an important research tool in biological research, fundamentally changing the traditional monoclonal antibody preparation process, and has been widely used in the establishment of antigen-antibody libraries, drug design, vaccine research, pathogen detection, gene therapy, antigenic epitope research, and cellular signal transduction research.The phage display is a powerful platform for technology development. Using phage display technology, single chain fragment variable (scFv) can be screened, replacing the disadvantage of the large size of traditional antibodies. Phage display single chain antibody libraries have significant biological implications. Here we describe the types of antibodies, including chimeric antibodies, bispecific antibodies, and scFvs. In addition, we describe the phage display system, phage display single chain antibody libraries, screening of specific antibodies by phage libraries and the application of phage libraries.

Combining CRISPR-Cas-mediated terminal resolution with a novel genetic workflow to achieve high-diversity adenoviral libraries.

While recombinant adenoviruses (rAds) are widely used in both laboratory and medical gene transfer, library-based applications using this vector platform are not readily available. Recently, we developed a new method, the CRISPR-Cas9 mediated in vivo terminal resolution aiding high-efficiency rescue of rAds from recombinant DNA. Here we report on a genetic workflow that allows construction of bacterial artificial chromosome-based rAd libraries reconstituted using highly efficient terminal resolution. We utilized frequent, pre-existing genomic sequences to allow the insertion of a selection marker, complementing two selected target sites into novel endonuclease recognition sites. In the second step, this selection marker is replaced with a transgene or mutation of interest via Gibson assembly. Our approach does not cause unwanted genomic off-target mutations while providing substantial flexibility for the site and nature of the genetic modification. This new genetic workflow, which we termed half site-directed fragment replacement (HFR) allows the introduction of more than 106 unique modifications into rAd encoding BACs using laboratory scale methodology. To demonstrate the power of HFR, we rescued barcoded viral vector libraries yielding a diversity of approximately 2.5 × 104 unique rAds per cm2 of transfected cell culture.

Genetically encoded libraries and spider venoms as emerging sources for crop protective peptides.

Agricultural crops are targeted by various pathogens (fungi, bacteria, and viruses) and pests (herbivorous arthropods). Antimicrobial and insecticidal peptides are increasingly recognized as eco-friendly tools for crop protection due to their low propensity for resistance development and the fact that they are fully biodegradable. However, historical challenges have hindered their development, including poor stability, limited availability, reproducibility issues, high production costs, and unwanted toxicity. Toxicity is a primary concern because crop-protective peptides interact with various organisms of environmental and economic significance. This review focuses on the potential of genetically encoded peptide libraries like the use of two-hybrid-based methods for antimicrobial peptides identification and insecticidal spider venom peptides as two main approaches for targeting plant pathogens and pests. We discuss some key findings and challenges regarding the practical application of each strategy. We conclude that genetically encoded peptide library- and spider venom-derived crop protective peptides offer a sustainable and environmentally responsible approach for addressing modern crop protection needs in the agricultural sector.

Unveiling Therapeutic Potential: Targeting Fusobacterium nucleatum's Lipopolysaccharide Biosynthesis for Endodontic Infections-An In Silico Screening Study.

Complex microbial communities have been reported to be involved in endodontic infections. The microorganisms invade the dental pulp leading to pulpitis and initiating pulp inflammation. Fusobacterium nucleatum is a dominant bacterium implicated in both primary and secondary endodontic infections. Drugs targeting the molecular machinery of F. nucleatum will minimize pulp infection. LpxA and LpxD are early acyltransferases involved in the formation of lipid A, a major component of bacterial membranes. The identification of leads which exhibit preference towards successive enzymes in a single pathway can also prevent the development of bacterial resistance. A stringent screening strategy utilizing physicochemical and pharmacokinetic parameters along with a virtual screening approach identified two compounds, Lomefloxacin and Enoxacin, with good binding affinity towards the early acyltransferases LpxA and LpxD. Lomefloxacin and Enoxacin, members of the fluoroquinolone antibiotic class, exhibit wide-ranging activity against diverse bacterial strains. Nevertheless, their effectiveness in the context of endodontic treatment requires further investigation. This study explored the potential of Lomefloxacin and Enoxacin to manage endodontic infections via computational analysis. Moreover, the compounds identified herein serve as a foundation for devising novel combinatorial libraries with enhanced efficacy for endodontic therapeutic strategies.